Construction of the Vicia sativa (common vetch) reference genome and exploration of genetic resources

Simple item page
dc.contributor.advisorSearle, lain
dc.contributor.advisorAustin, Jeremy
dc.contributor.authorXi, Hangwei
dc.contributor.schoolSchool of Biological Sciences
dc.date.issued2023
dc.description.abstractWith the continuous rise of the human population, exacerbated by global warming and water scarcity, humanity is facing a looming challenge in sustained food supply. In this context, Vicia sativa (common vetch), a crop characterized by high protein and nutritional value along with unique drought tolerance, is poised to become a successful human food source. However, the presence of antinutritional compounds like β-cyanoalanine (BCA) and γ-glutamyl-β-cyanoalanine (GBCA) in V. sativa seeds, which are toxic to monogastric organisms, currently restricts its use to green manure and ruminant livestock feed. As an overlooked orphon crop, the paucity of genomic resources for V. sativa has significantly hindered its breeding and conservation efforts. This study aims to collect and explore the genetic resources of V. sativa. In Chapter 2, I assembled the reference genome of V. sativa (n= 6). Utilizing 44x Oxford Nanopore sequencing data, the genome was assembled to contig level with a contig N50 of 684 kbp. Contigs were then polished with Illumina data, and finally assembled to chromosome level using Hi-C data. This assembly resulted in six chromosomes and two organelle genomes, with a complete BUSCO score of 98% and LAI of 12.96, indicating a high reference genome quality. Utilizing RNA-seq data, 53,218 genes were identified in the V. sativa genome. A shared whole-genome duplication event with legumes was identified, and the substitution rate of V. sativa was calculated as 8.02 × 10-9 per site per year. Chapter 3 presents a genome-wide variation map of 279 V. sativa samples. A significant population structure was observed within the V. sativa population, with the highest nucleotide diversity found in the Middle Eastern population, supporting the region as the center of origin for V. sativa. Selective sweep analysis revealed selection signals in multiple populations. For instance, positive selection of the VsSOC1/VsAGL20-like and the photoperiod-sensitive FTb2 gene in the higher latitude pop2 population suggests selective pressure on flowering time likely due to latitude variation. In Chapter 4, whole genome sequencing of the white seed coat gg1 mutant and green seed coat Lov2 variety led to the identification of two alleles of the VsA2 gene controlling seed coat color variation in V. sativa. In Lov2, a mutation of a highly conserved glycine to tryptophan amino acid mutation at position 153 in of the A2 protein likely causes the green color seed coat. In gg1, a 12 bp deletion in one of the functionally important WD40 domains in VsA2 was associated with the white seed coat phenotype. PCR analysis revealed that this deletion, also found in two other white-seeded varieties gg2 and gg3 discovered alongside gg1, indicate they are originated from the same mutation event.
dc.description.dissertationThesis (Ph.D.) -- University of Adelaide, School of Biological Sciences, 2024en
dc.identifier.urihttps://hdl.handle.net/2440/146597
dc.language.isoen
dc.provenanceThis thesis is currently under embargo and not available.en
dc.subjectVicia sativa
dc.subjectgenome assembly
dc.subjectcenter of diversity
dc.subjectdemographic history
dc.subjectpositive selection
dc.subjectseed coat color
dc.titleConstruction of the Vicia sativa (common vetch) reference genome and exploration of genetic resources
dc.typeThesisen

Files

Original bundle
Now showing 1 - 1 of 1
No Thumbnail Available
Name:
Xi2023_PhD.pdf
Size:
73.21 MB
Format:
Adobe Portable Document Format
Description:
Library staff access only.
Download

Collections

Research Theses